Population_template error

1

Hi everyone!

Could you possibly help me understand why I get the following error when I try to create a FOD population template?

population_template: [ERROR] Command failed: mrtransform /home/Fixel_Based_Analysis/fod_folder/subject.mif.gz -linear linear_transforms/subject.txt -datatype float32 input_transformed/subject_translated.mif

Cheers,
Vasiliki

2

I think we’ll need more information to answer that. What is the full error message?

3

Hi Max,

Please find below the script I run, and what appears on the terminal.

#!/bin/tcsh
# environment defaults
module load mrtrix/5.3.0
# working variables
set working_data=$HOME/COBRE_2/Fixel_Based_Analysis
population_template -verbose ${working_data}/fod_folder -mask_dir ${working_data}/upsampled_masks_folder ${working_data}/output_fod_template_image.mif.gz 



Command: mrregister /home/k1465455/COBRE_2/Fixel_Based_Analysis/fod_folder/A00024932.mif.gz average_header.mif.gz -mask1 /home/k1465455/COBRE_2/Fixel_Based_Analysis/upsampled_masks_folder/A00024932.mif.gz -rigid_scale 1  -rigid_niter 0  -type rigid  -noreorientation  -rigid_init_translation mass  -datatype float32 -rigid linear_transforms/A00024932.txt
mrregister: [100%] uncompressing image "/home/k1465455/COBRE_2/Fixel_Based_Analysis/fod_folder/A00024932.mif.gz"
mrregister: [100%] preloading data for "/home/k1465455/COBRE_2/Fixel_Based_Analysis/fod_folder/A00024932.mif.gz"
mrregister: [100%] uncompressing image "average_header.mif.gz"
mrregister: [100%] preloading data for "average_header.mif.gz"
mrregister: [  0%] uncompressing image "/home/k1465455/COBRE_2/Fixel_Based_Analysis/upsampled_masks_folder/A00024932.mif.mrregister: [ 50%] uncompressing image "/home/k1465455/COBRE_2/Fixel_Based_Analysis/upsampled_masks_folder/A00024932.mif.mrregister: [100%] uncompressing image "/home/k1465455/COBRE_2/Fixel_Based_Analysis/upsampled_masks_folder/A00024932.mif.mrregister: [100%] uncompressing image "/home/k1465455/COBRE_2/Fixel_Based_Analysis/upsampled_masks_folder/A00024932.mif.gz"
mrregister: running rigid registration
mrregister: initialising translation and centre of rotation using centre of mass
mrregister: multi-resolution level 1, scale factor 1
Command: mrtransform /home/k1465455/COBRE_2/Fixel_Based_Analysis/fod_folder/A00024932.mif.gz -linear linear_transforms/A00024932.txt -datatype float32 input_transformed/A00024932_translated.mif
mrtransform: SH series detected, performing apodised PSF reorientation
mrtransform: [100%] uncompressing image "/home/k1465455/COBRE_2/Fixel_Based_Analysis/fod_folder/A00024932.mif.gz"
mrtransform: [  0%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to "input_tran...ed/A00024932_translated.mif"mrtransform: [  1%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to "input_tran...ed/A00024932_translated.mif"mrtransform: [  2%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to "input_tran...ed/A00024932_translated.mif"mrtransform: [  3%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to "input_tran...ed/A00024932_translated.mif"mrtransform: [  4%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to 

....

"input_tran...ed/A00024932_translated.mif"mrtransform: [ 73%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to "input_tran...ed/A00024932_translated.mif"mrtransform: [ 74%] copying from "/home/k146...fod_folder/A00024932.mif.gz" to "input_tran...ed/A00024932_translated.mif"...... population_template: [ERROR] Command failed: mrtransform /home/k1465455/COBRE_2/Fixel_Based_Analysis/fod_folder/A00024932.mif.gz -linear linear_transforms/A00024932.txt -datatype float32 input_transformed/A00024932_translated.mif
population_template: Changing back to original directory (/home/k1465455/COBRE_2/Fixel_Based_Analysis)
population_template: Deleting temporary directory /tmp/population_template-tmp-BW8199/
[k1465455@nanlnx4 Fixel_Based_Analysis]1%

Cheers,
Vasiliki

4

This seems to be an old version of the script. Can you update to a current version and try again?

5

Is it possible that you have run out of space in /tmp? You can change the location of the temporary directory with -tempdir

Also, I am not sure what module you are using. What is mrtrix/5.3.0? The latest version I can see is:

module load mrtrix/0.3.15
/software/system/mrtrix/mrtrix-0.3.15/scripts/population_template ...
6

Hi Max,

I tried to update the newest version on my unix account but git pull doesn’t work.

Vasilikis-MacBook-Pro:nan vasilikichatzi$ cd mrtrix-0.3.15/
Vasilikis-MacBook-Pro:mrtrix-0.3.15 vasilikichatzi$ git pull
fatal: Not a git repository (or any parent up to mount point /Users/vasilikichatzi/nan)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Vasilikis-MacBook-Pro:mrtrix-0.3.15 vasilikichatzi$

Then I copied the population_template script from my mac to my unix account and I got this error:

[k1465455@nanlnx4 Fixel_Based_Analysis]0% study-specific_unbiased_FOD_template_FBA
ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'mrtrix/5.3.0’
Traceback (most recent call last):
File “/home/k1465455/mrtrix-0.3.15/scripts/population_template”, line 6, in
import lib.app, lib.cmdlineParser
ImportError: No module named cmdlineParser
[k1465455@nanlnx4 Fixel_Based_Analysis]1%

I should have enough space, I have 900 GB free.

I think I have to update mrtrix but I do not remember how to do it in unix.

Do you possibly remember how to update mrtrix in unix?

Cheers,
Vasiliki

7

For reference, here is what we did (following the instructions for static build) on my machine and then copied the folder mrtrix3 to your home directory:

git clone https://github.com/MRtrix3/mrtrix3.git
cd mrtrix3
ARCH='x86-64' ./configure -static -nogui
./build
./configure

Good luck!